Raw data for Mirarab et al. 2024 in PNAS: "A region of suppressed recombination misleads neoavian phylogenomics"

Supplementary data repository for the study by Mirarab et al. 2024 in PNAS: "A region of suppressed recombination misleads neoavian phylogenomics".This repository includes raw data used from the companion paper based on the Stiller et al. 2024 study (in press in Nature). The main analysis from this study is based on 63430 loci obtained from intergenic regions, maximum likelihood analysis, and coalescent-based species tree estimation, which are included in this repository. For more data analyses specific to this paper, please refer to https://zenodo.org/records/10699424Files and explanation of content:* 63430.alignments.tar.gz Alignments in FASTA format for which gene trees were built* 63430.gene.trees.gz Gene trees in newick format with support as aLRT values.* 63430.aLRT-0.95-collapsed.gene.trees.gz 63430 gene trees after collapsing branches with aLRT values below 0.95. This file was used as input for ASTRAL analysis.* 63430.named.gene.trees.gz Gene trees, with 1st column is name of the underlying locus, 2nd column is tree in newick format in order to match gene trees to alignments.* 63430.aLRT-0.95-collapsed.gene.trees.gz* 63430.ASTRAL.species.tre Main species tree resulting from ASTRAL analysis.* 63430.timetree.tre The time calibrated species tree.

补充数据仓库，用于 Mirarab 等人 2024 年在《PNAS》上发表的研究：“重组抑制区域误导了新鸟亚纲系统发育基因组学”。本仓库包含从基于 Stiller 等人 2024 年研究（即将在《Nature》杂志上发表）的配套论文中使用的原始数据。本研究的主要分析基于从基因间区域获得的 63,430 个位点，采用最大似然分析和基于谱系合并的物种树估计方法，这些数据均包含在本仓库中。有关本论文的更多数据分析方法，请参阅 https://zenodo.org/records/10699424Files 及内容说明：
* 63430.alignments.tar.gz：用于构建基因树的 FASTA 格式比对序列。
* 63430.gene.trees.gz：以 Newick 格式表示的基因树，其中包含作为 aLRT 值的支持。
* 63430.aLRT-0.95-collapsed.gene.trees.gz：经 aLRT 值低于 0.95 的分支合并后的 63,430 个基因树。该文件被用作 ASTRAL 分析的输入。
* 63430.named.gene.trees.gz：带有基因树，其中第一列是底层位点的名称，第二列是 Newick 格式的树，以便将基因树与比对序列匹配。
* 63430.ASTRAL.species.tre：ASTRAL 分析得出的主要物种树。
* 63430.timetree.tre：时间校准后的物种树。